1. Formation of a Highly Peptide-Receptive State of Class II MHC
Joshua D. Rabinowitz, Marija Vrljic, Peter M. Kasson, Michael N. Liang, Robert Busch, J.Jay Boniface, Mark M. Davis, Harden M. McConnell 
Immunity 
Volume 9, Issue 5, Pages (November 1998)
DOI: /S (00)

2. Figure 1
The Rate of Antigenic Peptide Binding to Empty sEk Is Not Accelerated by Increasing the Concentration of Added Peptide
The indicated concentration of fluorescently labeled MCC Ac was reacted with 100 nM {sEk}0 at pH 5.3, 37°C. After the indicated time, free peptide was separated from peptide/MHC complex by size exclusion chromatography, and labeled peptide/MHC complex formation was measured by a fluorescence detector.
Immunity 1998 9, DOI: ( /S (00) )

3. Figure 2
Dissociation of a Preformed Peptide/MHC Complex Generates Active sEk
In each panel, the starting material is 50 nM of the complex between sEk and the peptide indicated in bold on the panel. The filled circles indicate complex dissociation; the open circles, association of 5 μM labeled MCC Ac The dissociation axis represents the fraction of the initial complex remaining; the association axis, the fraction of total sEk bound by MCC. Both association and dissociation are at pH 5.3, 37°C. Solid lines are a single-exponential fit to the plotted data. For comparison to these data, peptide binding to {sEk}0 is only 1/3 complete after 120 min, the latest time shown in this figure (see Figure 1). In (C), peptide association appears to be slightly faster than peptide dissociation. This is likely because the unlabeled 8-mer peptide dissociates slightly faster than the labeled 8-mer peptide, presumably due to a hydrogen bond between the label and the MHC protein predicted based on the I-Ek crystal structure (Fremont et al. 1996). Also in (C), the association axis extends only to 0.6 units, because only half of the sEk produced by 8-mer dissociation is highly peptide receptive. (D) is a negative control which shows that a stable preformed peptide/MHC complex will not bind the added labeled peptide.
Immunity 1998 9, DOI: ( /S (00) )

4. Figure 3 Reversible Inactivation of Active sEk
(A) Formation of active sEk by peptide/MHC complex dissociation is followed by rapid sEk inactivation. 8-mer/sEk complex was incubated at pH 5.3 and 37°C for the indicated “delay time” in the absence of added peptide. The amount of active sEk present after the delay was measured by the binding of 5 μM labeled MCC for 5 min. The solid line indicates the analytical solution to the system of differential equations describing reaction scheme (3) (see Experimental Procedures), with the half-life of active sEk of 13 min. Errors bars indicate the standard error of triplicate measurements after delays of 10 min and 40 min.
(B) Inactive sEk slowly reverts to active sEk. Shaded bars depict the binding of labeled MCC to inactive sEk formed by incubating CLIP/sEk complex in the absence of peptide for 2 hr at pH 5.3, 37°C prior to the MCC addition. Solid bars are the positive control depicting the binding of labeled MCC to CLIP/sEk complex. CLIP/sEk is at 50 nM; labeled MCC at 100 nM; similar data have been obtained for MCC concentrations up to 50 μM. Error bars indicate the standard error of duplicate measurements.
Immunity 1998 9, DOI: ( /S (00) )

5. Figure 4 Rapid Binding of Several Different Peptides to Active sEk
A solution containing approximately 25% active sEk (total sEk concentration 8 nM) was formed by allowing 8-mer/sEk complex to dissociate in the absence of added peptide for 5 min at pH 5.3, 37°C. At this point, the labeled peptide indicated in the figure legend was added and allowed to bind for 3 min. Lines indicate a single exponential fit to the data with kon ≈ 5 × 105 M−1 s−1 (range 4–6 × 105 M−1 s−1) for each peptide (see Experimental Procedures).
Immunity 1998 9, DOI: ( /S (00) )

6. Figure 5
Dissociation of a Preformed Peptide/sDR1 Complex Generates Active sDR1
(A) Binding of the indicated concentration of fluorescently labeled influenza hemagglutinin peptide (HA) to 100 nM {sDR1}0 at pH 5.3 and 37°C.
(B) Binding of the indicated concentration of HA to preformed 8-mer/sDR1 complex (50 nM) at pH 5.3 and 37°C. 8-mer is MCC Ac
(C) Formation of active sDR1 (sDR1a) by peptide/MHC complex dissociation is followed by rapid sDR1 inactivation. The indicated concentration of 8-mer/sDR1 complex was incubated at pH 5.3, 37°C for the indicated “delay time” in the absence of added peptide. The amount of active sDR1 present after the delay was measured by the binding of 1 μM labeled HA for 5 min. The solid line indicates the analytical solution to the system of differential equations describing reaction scheme (3) (see Experimental Procedures), with the half-life of active sDR1 of 4 min for the 17 nM sDR1 and 6 min for the 50 nM sDR1.
Immunity 1998 9, DOI: ( /S (00) )

7. Figure 6 Reactions of sEk at pH 7.0
(A) Dissociation of a preformed peptide/sEk complex generates active sEk. Analogous to Figure 2B, starting material is 50 nM of the complex between sEk and CLIP M90L M98L. The filled circles indicate complex dissociation; the open circles, the association of 5 μM labeled MCC Ac Solid lines are a single-exponential fit to the plotted data. For comparison, 5 μM MCC Ac binding to empty {sEk}0 is shown as the open squares and dashed line.
(B) Peptide concentration dependence of sEka binding at pH 7.0. The indicated concentration of fluorescently labeled MCC Ac was reacted with 100 nM CLIP M90L M98L/sEk complex at 37°C, and the binding after 20 min was compared to the binding of saturating concentrations of labeled MCC (100–300 μM).
Immunity 1998 9, DOI: ( /S (00) )

8. Figure 7
T Cell Stimulation by Fixed APCs Preloaded with Various Peptides
(A) Enhanced T cell acid release by APCs preloaded with a peptide that rapidly dissociates from I-Ek, CLIP M90L M98L. Fixed CH27 cells were incubated at pH 5.3, 37°C for 20 hr in either presence or absence of 200 μM of this CLIP mutant. After this time, the APCs were washed and mixed with 5C.C7 T cells. The T cells response to a 3 min exposure to the indicated concentration of MCC Ac peptide was then measured based on increases in the rate of T cell acid release over the subsequent 9 min.
(B) Dissociation of a preformed peptide/MHC complex generates active I-Ek on the cell surface (summary of data presented in [A]). Data points represent the percent increase in acid release rate 12 min after addition of MCC peptide. The line indicates a log-linear fit to the data. The label “12.6-fold” indicates that a 12.6-fold greater concentration of peptide was required to produce a given level of acid release using the no peptide treated APCs as compared to the mutated CLIP treated APCs. Similar results were obtained in three independent experiments.
(C) Formation of active I-Ek by peptide/MHC complex dissociation is followed by rapid I-Ek inactivation. Fixed CH27 cells were incubated at pH 5.3, 37°C for 20 hr in the presence of 200 μM CLIP M90L M98L. The APCs were then washed and incubated for additional 60 min, under the same conditions, in either the presence or absence of 200 μM of this peptide, and T cell stimulation was measured as described above. Incubation of the APCs in the absence of peptide for 60 min resulted in a ≥3-fold shift in the T cell dose response in four independent experiments.
(D) Inactive I-Ek on the cell surface slowly reverts to active I-Ek.
Fixed CH27 cells were incubated at pH 5.3, 37°C for 30 hr in either the presence or absence of a peptide that binds stably to I-Ek, BEK (for details on BEK, see Experimental Procedures). The APCs were then washed and incubated for additional 100 min, under the same conditions, in the absence of BEK, and T cell stimulation was measured as described above. Similar results were obtained in three independent experiments.
Immunity 1998 9, DOI: ( /S (00) )